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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcattattttaaactattttctgtaatccgtaacttgcaacaagatttttctcactgttctagatcctgattgcagagtgtgcttattgtttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGGGTGGAGAATGTGCTTTTGGAGGAGGGAAATGCTACAATTCTGACCCTCT

Basic information

species Glycine max
transcript GLYMA08G05930.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G05930.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g02280.t01 (Vitis vinifera), 3'ss of exon 5
gtcattattttaaactattttctgtaatccgtaacttgcaacaagatttttctcactgttctagatcctga--ttgcagagtgtgcttattgtttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGGGTGGAGAATGTGCTTTTGGAGGAGGGAAATGCTACAATTCTGACCCTCT
    |  | | |    | ||| || | |   ||| | |  | ||      ||||  |  ||  |||  |||  |    |  | ||    | | |||||||||||  |  |  | |||||| |||||||| | ||||| ||| | ||||| ||||||||||||||| |  ||||||| |||||||| |||||||| ||||| |
--tgtcttctcatttaagtttttgaattttttaaatagagaaaaagggaatctccattctcaggattatgaactgattggatttgtgcttgggttttattagGTTGACTTGGTCGATTCACTGCCTGAAGTCTATCCAAAAGTGGAAGCATGGGTGGAGAATGTGATCATGGAGGAAGGAAATGCAACAATTCTCACCCTTT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|193675801|gb|FK615783.1|FK615783
EST:     TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATG                         GTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
genomic: TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATGgtgagtttct ... tttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
EST: gi|7233239|gb|AW568587.1|AW568587
EST:     TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATG                         GTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
genomic: TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATGgtgagtttct ... tttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
EST: gi|192329412|gb|FK021838.1|FK021838
EST:     TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATG                         GTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
genomic: TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATGgtgagtttct ... tttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
EST: gi|209697397|gb|BW675542.1|BW675542
EST:     TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATG                         GTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
genomic: TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATGgtgagtttct ... tttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
EST: gi|254324939|gb|GR834364.1|GR834364
EST:     TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATG                         GTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
genomic: TGGCTCTTTCAAGCCTGTGGGTTCGTAAGAACTATGCTGACAGTTTCATGgtgagtttct ... tttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
EST: gi|207811072|gb|GD782993.1|GD782993
EST:     CTGACAGTTTCATG                         GTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG
genomic: CTGACAGTTTCATGgtgagtttct ... tttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctcactgttctagatcctgattgcagagtgtgcttattgtttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGGGTGGAGAATGTGCTTTTGGAGGAGGGAAATGCTACAATTCTGACCCTCT
                                          ttgttttt  CT-rich tract
                                       ttattgtttttatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattattttaaactattttctgtaatccgtaacttgcaacaagatttttctcactgttctagatcctgattgcagagtgtgcttattgtttttattagGTACAGGTAATTGATTCATTGCCTGAACTGTATCCTAAATTAGAAGCTTGGGTGGAGAATGTGCTTTTGGAGGAGGGAAATGCTACAATTCTGACCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG